Installation

Stable version

Stable versions of SnapATAC2 are published on PyPI. Precompiled binaries are available for x86_64 Linux systems and macOS. So installing it is as simple as running:

pip install snapatac2

If there are no precompiled binaries published for your system, you will have to build the package from source. Building the SnapATAC2 library requires cmake >= 3.5.1 and the Rust compiler. You need to install them first if they are not available on your system. You can find the instructions for installing cmake here. The Rust compiler can be installed using:

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
rustup default nightly

Once you have cmake and the Rust compiler properly installed, running pip install snapatac2 will build SnapATAC2 from the source package and install it just as it would if there was a prebuilt binary available.

Nightly build

The nightly build is the build from the latest source codes, which includes the latest features, enhancements, and bug fixes that haven’t been released. The nightly build can be unstable and include some untested features.

You can download the wheel files of the latest Nightly build from this link.

After downloading the file, unzip it and then select the appropriate wheel file for your platform and use pip install to install it.

Build from the latest source code

Building the SnapATAC2 library requires cmake >= 3.5.1 and the Rust compiler. You need to install them first if they are not available on your system. You can find the instructions for installing cmake here. The Rust compiler can be installed using:

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
rustup default nightly

Once you have cmake and the Rust compiler properly installed, clone the source code repository and go to the snapatac2-python directory, use pip install . to install the package.

git clone https://github.com/kaizhang/SnapATAC2.git
cd SnapATAC2/snapatac2-python
pip install .

Optional dependencies

Here is a list of optional dependencies used by SnapATAC2:

• macs2: Peak calling.

• harmonypy: Batch correction using the Harmony.

• xgboost: Regulatory network analysis.

Optional dependencies are not installed by SnapATAC2. Please install them manually if necessary.